test/jalview/bin/commandsTest.jvprops

   1 #---JalviewX Properties File---
   2 #Fri Apr 25 09:54:25 BST 2014
   3 SCREEN_Y=768
   4 SCREEN_X=936
   5 SHOW_WSDISCOVERY_ERRORS=true
   6 LATEST_VERSION=2.8.0b1
   7 JALVIEW_RSS_WINDOW_SCREEN_WIDTH=550
   8 JAVA_CONSOLE_SCREEN_WIDTH=450
   9 LAST_DIRECTORY=/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples
  10 ID_ITALICS=true
  11 SORT_ALIGNMENT=No sort
  12 WSMENU_BYHOST=false
  13 SEQUENCE_LINKS=EMBL-EBI Search|http\://www.ebi.ac.uk/ebisearch/search.ebi?db\=allebi&query\=$SEQUENCE_ID$
  14 SHOW_FULLSCREEN=false
  15 RECENT_URL=http\://www.jalview.org/examples/exampleFile_2_7.jar
  16 FONT_NAME=SansSerif
  17 BLC_JVSUFFIX=true
  18 VERSION_CHECK=false
  19 YEAR=2011
  20 SHOW_DBREFS_TOOLTIP=true
  21 MSF_JVSUFFIX=true
  22 SCREENGEOMETRY_HEIGHT=1600
  23 JAVA_CONSOLE_SCREEN_Y=475
  24 JAVA_CONSOLE_SCREEN_X=830
  25 PFAM_JVSUFFIX=true
  26 PIR_JVSUFFIX=true
  27 STARTUP_FILE=http\://www.jalview.org/examples/exampleFile_2_3.jar
  28 JAVA_CONSOLE_SCREEN_HEIGHT=162
  29 PIR_MODELLER=false
  30 GAP_SYMBOL=-
  31 SHOW_QUALITY=true
  32 SHOW_GROUP_CONSERVATION=false
  33 SHOW_JWS2_SERVICES=true
  34 SHOW_NPFEATS_TOOLTIP=true
  35 FONT_STYLE=plain
  36 ANTI_ALIAS=false
  37 SORT_BY_TREE=false
  38 RSBS_SERVICES=|Multi-Harmony|Analysis|Sequence Harmony and Multi-Relief (Brandt et al. 2010)|hseparable,gapCharacter\='-',returns\='ANNOTATION'|?tool\=jalview|http\://zeus.few.vu.nl/programs/shmrwww/index.php?tool\=jalview&groups\=$PARTITION\:min\='2',minsize\='2',sep\=' '$&ali_file\=$ALIGNMENT\:format\='FASTA',writeasfile$
  39 AUTHORFNAMES=Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
  40 JALVIEW_RSS_WINDOW_SCREEN_HEIGHT=328
  41 SHOW_GROUP_CONSENSUS=false
  42 SHOW_CONSENSUS_HISTOGRAM=true
  43 SHOW_OVERVIEW=false
  44 AUTHORS=J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  45 FIGURE_AUTOIDWIDTH=false
  46 SCREEN_WIDTH=900
  47 ANNOTATIONCOLOUR_MIN=ffc800
  48 SHOW_STARTUP_FILE=false
  49 RECENT_FILE=examples/uniref50.fa\t/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples/RF00031_folded.stk\t/Volumes/Data/Users/jimp/bs_ig_mult.out
  50 DEFAULT_FILE_FORMAT=FASTA
  51 SHOW_JAVA_CONSOLE=false
  52 VERSION=2.8b1
  53 FIGURE_USERIDWIDTH=
  54 WSMENU_BYTYPE=false
  55 DEFAULT_COLOUR=None
  56 NOQUESTIONNAIRES=true
  57 JALVIEW_NEWS_RSS_LASTMODIFIED=Apr 23, 2014 2\:53\:26 PM
  58 BUILD_DATE=01 November 2013
  59 PILEUP_JVSUFFIX=true
  60 SHOW_CONSENSUS_LOGO=false
  61 SCREENGEOMETRY_WIDTH=2560
  62 JALVIEW_RSS_WINDOW_SCREEN_Y=0
  63 USAGESTATS=false
  64 JALVIEW_RSS_WINDOW_SCREEN_X=0
  65 SHOW_UNCONSERVED=false
  66 SHOW_JVSUFFIX=true
  67 DAS_LOCAL_SOURCE=
  68 SCREEN_HEIGHT=650
  69 ANNOTATIONCOLOUR_MAX=ff0000
  70 AUTO_CALC_CONSENSUS=true
  71 FASTA_JVSUFFIX=true
  72 DAS_ACTIVE_SOURCE=uniprot\t
  73 JWS2HOSTURLS=http\://www.compbio.dundee.ac.uk/jabaws
  74 PAD_GAPS=false
  75 CLUSTAL_JVSUFFIX=true
  76 SHOW_ENFIN_SERVICES=true
  77 FONT_SIZE=10
  78 RIGHT_ALIGN_IDS=false
  79 USE_PROXY=false
  80 WRAP_ALIGNMENT=false
  81 #DAS_REGISTRY_URL=http\://www.dasregistry.org/das/ # retired 01/05/2015
  82 DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/
  83 SPLASH=false
  84 ADD_SS_ANN=true
  85 ADD_TEMPFACT_ANN=true
  86 SHOW_ANNOTATIONS=true
  87 SHOW_CONSERVATION=true
  88 SHOW_IDENTITY=true
  89 SHOW_OCCUPANCY=true
  90 STRUCT_FROM_PDB=true